Abstract: Transcriptome polymorphism is an important aspect for species diversity and species molecular evolution. HSP70 and HSP90 are high-conserved in eukaryotic species. In the study, we analyzed the gene structural variation about hsp70 and hsp90, and the phylogenetic relationships between Bursaphelenchus xylophilus and B. mucronatus. The results showed that parallels and distinctions coexisted in both hsp genes of B. xylophilus and B. mucronatus. Both HSP70s shared 99% similarities, and only 9 of 642 amino acids showed differences in both high-conserved amino sequences, which were caused by 13 nucleic acid bases. Meanwhile, HSP90s possessed of 92% similarities in B. xylophilus and B. mucronatus. There were differences in the 10 codons encoding 17 amino acids between gABG and gmc2, while gABO and gmc19 showed differences in the 5 codons. These diversities were valuable for species diversity and molecular evolution. Moreover, the phylogenetic trees of hsp70 and hsp90 showed high homology of B. xylophilus and B. mucronatus with other nemathelminthes species.